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[audio]Genetics 10/1
Genetics lecture on October, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 40
[audio]Genetics 10/13
Genetics lecture on October 13, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 62
[audio]Genetics 11/10
Genetics lecture on November 10, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 28
[texts]Comparison of Y-chromosomal lineage dating using either evolutionary or genealogical Y-STR mutation rates - Chuan-Chao Wang
We have compared the Y chromosomal lineage dating between sequence data and commonly used Y-SNP plus Y-STR data. The coalescent times estimated using evolutionary Y-STR mutation rates correspond best with sequence-based dating when the lineages include the most ancient haplogroup A individuals. However, the times using slow mutated STR markers with genealogical rates fit well with sequence-based estimates in main lineages, such as haplogroup CT, DE, K, NO, IJ, P, E, C, I, J, N, O, and R...
Keywords: Genetics
[texts]Cell specific eQTL analysis without sorting cells - Harm-Jan Westra
Expression quantitative trait locus (eQTL) mapping on tissue, organ or whole organism data can detect associations that are generic across cell types. We describe a new method to focus upon specific cell types without first needing to sort cells. We applied the method to whole blood data from 5,683 samples and demonstrate that SNPs associated with Crohns disease preferentially affect gene expression within neutrophils.
Keywords: Genetics
[texts]Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences - Sebastian Lippold
To investigate in detail the paternal and maternal demographic histories of humans, we obtained ~500 kb of non-recombining Y chromosome (NRY) sequences and complete mtDNA genome sequences from 623 males from 51 populations in the CEPH Human Genome Diversity Panel (HGDP). Our results: confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA; suggest very small ancestral effective population sizes (
Keywords: Genetics
[texts]Human genetics and clinical aspects of neurodevelopmental disorders - Gholson J Lyon
There are ~12 billion nucleotides in every cell of the human body, and there are ~25-100 trillion cells in each human body. Given somatic mosaicism, epigenetic changes and environmental differences, no two human beings are the same, particularly as there are only ~7 billion people on the planet. One of the next great challenges for studying human genetics will be to acknowledge and embrace complexity...
Keywords: Genetics
[texts]The Genetic Legacy of the Expansion of Turkic-Speaking Nomads Across Eurasia - Bayazit Yunusbayev
The Turkic peoples represent a diverse collection of ethnic groups defined by the Turkic languages. These groups have dispersed across a vast area, including Siberia, Northwest China, Central Asia, East Europe, the Caucasus, Anatolia, the Middle East, and Afghanistan. The origin and early dispersal history of the Turkic peoples is disputed, with candidates for their ancient homeland ranging from the Transcaspian steppe to Manchuria in Northeast Asia...
Keywords: Genetics
[texts]Variational Inference of Population Structure in Large SNP Datasets - Anil Raj
Tools for estimating population structure from genetic data are now used in a wide variety of applications in population genetics. However, inferring population structure in large modern data sets imposes severe computational challenges. Here, we develop efficient algorithms for approximate inference of the model underlying the STRUCTURE program using a variational Bayesian framework. Variational methods pose the problem of computing relevant posterior distributions as an optimization problem, a...
Keywords: Genetics
[texts]Genetic influences on translation in yeast - Frank W. Albert
Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosome profiling to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes...
Keywords: Genetics
[texts]OTX2 Dosage Sensitivity is Implicated in Hemifacial Microsomia - Dina Zielinski
Hemifacial microsomia (HFM) is the second most common facial anomaly after cleft lip and palate. The phenotype is highly variable and most cases are sporadic. Here, we investigated the disorder in a large pedigree with five affected individuals spanning eight meioses. We performed whole-exome sequencing and a genome-wide survey of segmental variations. Analysis of the exome sequencing results indicated the absence of a pathogenic coding point mutation...
Keywords: Genetics
[texts]Robust Population Structure Inference and Correction in the Presence of Known or Cryptic Relatedness - Matthew P Conomos
Population structure inference with genetic data has been motivated by a variety of applications in population genetics and genetic association studies. Several approaches have been proposed for the identification of genetic ancestry differences in samples where study participants are assumed to be unrelated, including principal components analysis (PCA), multi-dimensional scaling (MDS), and model-based methods for proportional ancestry estimation...
Keywords: Genetics
[texts]Efficient Bayesian mixed model analysis increases association power in large cohorts - Po-Ru Loh
Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts, and may not optimize power. All existing methods require time cost O(MN^2) (where N = #samples and M = #SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power...
Keywords: Genetics
[texts]Dead or just asleep? Variance of microsatellite allele distributions in the human Y-chromosome. - Joe Flood
Several different methods confirm that a number of micro-satellites on the human Y-chromosome have allele distributions with different variances in different haplogroups, after adjusting for coalescent times. This can be demonstrated through both heteroscedasticity tests and by poor correlation of the variance vectors in different subclades. The most convincing demonstration however is the complete inactivity of some markers in certain subclades – “microsatellite death”, while they are sti...
Keywords: Genetics
[texts]Estimating strength of polygenic selection with principal components analysis of spatial genetic variation - Davide Piffer
Principal components analysis on allele frequencies for 14 and 50 populations (from 1K Genomes and ALFRED databases) produced a factor accounting for over half of the variance, which indicates selection pressure on intelligence or genotypic IQ. Very high correlations between this factor and phenotypic IQ, educational achievement were observed (r>0.9 and 0.8), also after partialling out GDP and the Human Development Index...
Keywords: Genetics
[texts]Genetic dissection of MAPK-mediated complex traits across S. cerevisiae - Sebastian Treusch
Signaling pathways enable cells to sense and respond to their environment. Many cellular signaling strategies are conserved from fungi to humans, yet their activity and phenotypic consequences can vary extensively among individuals within a species. A systematic assessment of the impact of naturally occurring genetic variation on signaling pathways remains to be conducted. In S. cerevisiae , both response and resistance to stressors that activate signaling pathways differ between diverse isolate...
Keywords: Genetics
[texts]Reconstructing Austronesian population history in Island Southeast Asia - Mark Lipson
Austronesian languages are spread across half the globe, from Easter Island to Madagascar. Evidence from linguistics and archaeology indicates that the "Austronesian expansion," which began 4-5 thousand years ago, likely had roots in Taiwan, but the ancestry of present-day Austronesian-speaking populations remains controversial. Here, focusing primarily on Island Southeast Asia, we analyze genome-wide data from 56 populations using new methods for tracing ancestral gene flow...
Keywords: Genetics
[texts]Spatial localization of recent ancestors for admixed individuals - Wen-Yun Yang
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over non-model-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum...
Keywords: Genetics
[texts]Cosi2 : An efficient simulator of exact and approximate coalescent with selection - Ilya Shlyakhter
Motivation: Efficient simulation of population genetic samples under a given demographic model is a prerequisite for many analyses. Coalescent theory provides an efficient framework for such simulations, but simulating longer regions and higher recombination rates remains challenging. Simulators based on a Markovian approximation to the coalescent scale well, but do not support simulation of selection...
Keywords: Genetics
[audio]Genetics 10/8
Genetics lecture on October 8, 2008 at North Park University with Dr. Schau.
Keywords: genetics
Downloads: 44
[texts]Calling genotypes from public RNA-sequencing data enables identification of genetic variants that affect gene-expression levels - Patrick Deelen
Given increasing numbers of RNA-seq samples in the public domain, we studied to what extent expression quantitative trait loci (eQTLs) and allele-specific expression (ASE) can be identified in public RNA-seq data while also deriving the genotypes from the RNA-seq reads. 4,978 human RNA-seq runs, representing many different tissues and cell-types, passed quality control. Even though this data originated from many different laboratories, samples reflecting the same cell-type clustered together, su...
Keywords: Genetics
[texts]Genetics - Shull, George Harrison, 1874-
Book digitized by Google from the library of Harvard University and uploaded to the Internet Archive by user tpb.
Keywords: Genetics
Downloads: 231
[texts]Differential relationships between habitat fragmentation and within-population genetic diversity of three forest-dwelling birds - Benjamin Zuckerberg
Habitat fragmentation is a major driver of environmental change affecting wildlife populations across multiple levels of biological diversity. Much of the recent research in landscape genetics has focused on quantifying the influence of fragmentation on genetic variation among populations, but questions remain as to how habitat loss and configuration influences within-population genetic diversity. Habitat loss and fragmentation might lead to decreases in genetic diversity within populations, whi...
Keywords: Genetics
[texts]Efficient site-specific editing of the C. elegans genome - Donglei Zhang
In just two years, genome editing with the CRISPR-associated endonuclease Cas9 has transformed genetic analysis in conventional and emerging model organisms. The efficiency of this method varies among systems and continues to be optimized. Numerous strategies have been reported for editing the C. elegans genome. To date, these strategies do not provide a simple, rapid and inexpensive means to introduce and isolate arbitrary point mutants...
Keywords: Genetics
[texts]Theoretical genetics - Goldschmidt, Richard Benedict, 1878-1958
Bibliography: p. 494-544
Keywords: Genetics
Downloads: 987
[texts]Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function - John F Mulley
Background Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles, although the lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancre...
Keywords: Genetics
[texts]Behavioral individuality reveals genetic control of phenotypic variability - Julien F Ayroles
Variability is ubiquitous in nature and a fundamental feature of complex systems. Few studies, however, have investigated variance itself as a trait under genetic control. By focusing primarily on trait means and ignoring the effect of alternative alleles on trait variability, we may be missing an important axis of genetic variation contributing to phenotypic differences among individuals. To study genetic effects on individual-to-individual phenotypic variability (or intragenotypic variability)...
Keywords: Genetics
Downloads: 4
[audio]Good Health
terms
Keywords: Genetics
Downloads: 2
[texts]A Tale of Two Hypotheses: Genetics and the Ethnogenesis of Ashkenazi Jewry - Aram Yardumian
The debate over the ethnogenesis of Ashkenazi Jewry is longstanding, and has been hampered by a lack of Jewish historiographical work between the Biblical and the early Modern eras. Most historians, as well as geneticists, situate them as the descendants of Israelite tribes whose presence in Europe is owed to deportations during the Roman conquest of Palestine, as well as migration from Babylonia, and eventual settlement along the Rhine...
Keywords: Genetics
Downloads: 4
[texts]Heteroplasmy is ubiquitous and stable at the single cell level - Anitha D Jayaprakash
Eukaryotic cells carry two genomes, nuclear (nDNA) and mitochondrial (mtDNA), which are ostensibly decoupled in their replication, segregation and inheritance. It is increasingly appreciated that heteroplasmy, the occurrence of multiple mtDNA haplotypes in a cell, plays an important biological role, but its features are not well understood. Until now, accurately determining the diversity of mtDNA has been difficult due to the relatively small amount of mtDNA in each cell ( 98%) mtDNA and its abi...
Keywords: Genetics
[texts]Approximation to the distribution of fitness effects across functional categories in human segregating polymorphisms - Fernando Racimo
Quantifying the proportion of polymorphic mutations that are deleterious or neutral is of fundamental importance to our understanding of evolution, disease genetics and the maintenance of variation genome-wide. Here, we develop an approximation to the distribution of fitness effects (DFE) of segregating single-nucleotide mutations in humans. Unlike previous methods, we do not assume that synonymous mutations are neutral or not strongly selected, and we do not rely on fitting the DFE of all new n...
Keywords: Genetics
Downloads: 2
[texts]The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20 - Morgan Price
Sulfate-reducing bacteria play major roles in the global carbon and sulfur cycles, but it remains unclear how reducing sulfate yields energy. To determine the genetic basis of energy conservation, we measured the fitness of thousands of pooled mutants of Desulfovibrio alaskensis G20 during growth in 12 different combinations of electron donors and acceptors. We show that ion pumping by the ferredoxin:NADH oxidoreductase Rnf is required whenever substrate-level phosphorylation is not possible...
Keywords: Genetics
Downloads: 1
[texts]An introduction to modern genetics - Waddington, C. H. (Conrad Hal), 1905-1975
"Bibliography and author-index": p. [409]-434
Keywords: Genetics
Downloads: 1,834
[texts]Genetic variants associated with motion sickness point to roles for inner ear development, neurological processes, and glucose homeostasis - Bethann S Hromatka
Roughly one in three individuals is highly susceptible to motion sickness and yet the underlying causes of this condition are not well understood. Despite high heritability, no associated genetic factors have been discovered to date. Here, we conducted the first genome-wide association study on motion sickness in 80,494 individuals from the 23andMe database who were surveyed about car sickness. Thirty-five single-nucleotide polymorphisms (SNPs) were associated with motion sickness at a genome-wi...
Keywords: Genetics
Downloads: 2
[texts]Elementary genetics - Singleton, W. Ralph
http://uf.catalog.fcla.edu/uf.jsp?st=UF000754868&ix=nu&I=0&V=D
Keywords: Genetics
Downloads: 3,484
[texts]Regulatory variants explain much more heritability than coding variants across 11 common diseases - Alexander Gusev
Common variants implicated by genome-wide association studies (GWAS) of complex diseases are known to be enriched for coding and regulatory variants. We applied methods to partition the heritability explained by genotyped SNPs (h2g) across functional categories (while accounting for shared variance due to linkage disequilibrium) to genotype and imputed data for 11 common diseases. DNaseI Hypersensitivity Sites (DHS) from 218 cell-types, spanning 16% of the genome, explained an average of 79% of ...
Keywords: Genetics
Downloads: 7
[texts]Sexual dimorphism in epigenomic responses of stem cells to extreme fetal growth - Fabien Delahaye
Extreme fetal growth is associated with increased susceptibility to a range of adult diseases through an unknown mechanism of cellular memory. We tested whether heritable epigenetic processes in long-lived CD34+ hematopoietic stem/progenitor cells (HSPCs) showed evidence for re-programming associated with the extremes of fetal growth. Here we show that both fetal growth restriction and over-growth are associated with global shifts towards DNA hypermethylation, targeting cis-regulatory elements i...
Keywords: Genetics
Downloads: 2
[texts]ESTIMATION OF (CO)VARIANCE COMPONENTS BY WEIGHTED AND UNWEIGHTED SYMMETRIC DIFFERENCES SQUARED, AND SELECTED MIVQUE'S: RELATIONSHIPS BETWEEN METHODS AND RELATIVE EFFICIENCIES - John W Keele
PhD dissertation, Ohio State University
Keywords: genetics
Downloads: 97
[collection]Genetics - Genetics

Keywords: Genetics
Downloads: 4,219
[audio]Genetics Lecture 7, 9/12: Review for Test 1
Genetics Lecture 7, 9/12: Review for Test 1 with Dr. Schau at North Park University.
Keywords: genetics
Downloads: 67
[texts]Genetics; an introduction to the study of heredity - Walter, Herbert Eugene, b. 1867
Book digitized by Google from the library of University of Michigan and uploaded to the Internet Archive by user tpb.
Keywords: Genetics
Downloads: 202
[texts]Different tastes for different individuals - Kohei Fujikura
Individual taste differences were first reported in the first half of the 20th century, but the primary reasons for these differences have remained uncertain. Much of the taste variation among different mammalian species can be explained by pseudogenization of taste receptors. In this study, by analyzing 14 ethnically diverse populations, we investigated whether the most recent disruptions of taste receptor genes segregate with their intact forms...
Keywords: Genetics
Downloads: 1
[texts]The elements of genetics - Darlington, C. D. (Cyril Dean), 1903-
Includes bibliographies and index
Keywords: Genetics
Downloads: 2,349
[texts]Stress, heritability, tissue type and human methylome variation in mother-newborn dyads. - David A. Hughes
DNA methylation variation has been implicated as a factor that influences inter-individual and inter-tissue phenotypic variation in numerous organisms and under various conditions. Here, using a unique collection of three tissues, derived from 24 mother-newborn dyads from war-torn Democratic Republic of Congo, we estimate how stress, heritability, tissue type and genomic/regulatory context influence genome-wide DNA methylation...
Keywords: Genetics
Downloads: 3
[audio]Genetics 9/22
Genetics lecture with Dr. Schau at North Park University on September 22, 2008 discussing linkage mapping in Eukaryotes. http://genetics3210.blogspot.com/
Keywords: genetics
Downloads: 29
[texts]Dictionary of genetics, including terms used in cytology, animal breeding and evolution - Knight, Robert L., 1907-
Bibliography: p. [179]-183
Keywords: Genetics
Downloads: 2,681
[texts]Selection signatures in worldwide Sheep populations - Maria-Ines Fariello
The diversity of populations in domestic species offers great opportunities to study genome response to selection. The recently published Sheep HapMap dataset is a great example of characterization of the world wide genetic diversity in sheep. In this study, we re-analyzed the Sheep HapMap dataset to identify selection signatures in worldwide sheep populations. Compared to previous analyses, we made use of statistical methods that (i) take account of the hierarchical structure of sheep populatio...
Keywords: Genetics
Downloads: 5
[texts]Inferring human population size and separation history from multiple genome sequences - Stephan Schiffels
The availability of complete human genome sequences from populations across the world has given rise to new population genetic inference methods that explicitly model their ancestral relationship under recombination and mutation. So far, application of these methods to evolutionary history more recent than 20-30 thousand years ago and to population separations has been limited. Here we present a new method that overcomes these shortcomings...
Keywords: Genetics
[texts]When genomes collide: multiple modes of germline misregulation in a dysgenic syndrome of Drosophila virilis - Mauricio A. Galdos
In sexually reproducing species the union of gametes that are not closely related can result in genomic incompatibility. Hybrid dysgenic syndromes represent a form of genomic incompatibility that can arise when transposable element (TE) abundance differs between two parents. When TEs lacking in the female parent are transmitted paternally, a lack of corresponding silencing small RNAs (piRNAs) transmitted through the female germline can lead to TE mobilization in progeny...
Keywords: Genetics
[texts]The overdue promise of short tandem repeat variation for heritability. - Maximilian Press
Short tandem repeat (STR) variation has been proposed as a major explanatory factor in the heritability of complex traits in humans and model organisms. However, we still struggle to incorporate STR variation into genotype-phenotype maps. Here, we review the promise of STRs in contributing to complex trait heritability, and highlight the challenges that STRs pose due to their repetitive nature. We argue that STR variants are more likely than single nucleotide variants to have epistatic interacti...
Keywords: Genetics
Downloads: 1
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